Question: How to visualize the data
0
gravatar for mayurdoke
18 months ago by
mayurdoke10
mayurdoke10 wrote:

Hi all,

enter image description hereAm I missing plugin to visualize the data

software error galaxy • 872 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by mayurdoke10

Related question: https://biostar.usegalaxy.org/p/23361/

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
1
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The image shared is not publically accessible. I am guessing that either no visualization options are available for the currently assigned datatype, the datatype is still non-specific (example: .txt) or that you do not know where to find them based on your other post (https://biostar.usegalaxy.org/p/23361/).

  • First, assign the correct datatype to the dataset(s).
  • Second, assign the correct database (genome build) to the dataset. This is needed for some options.
  • After this, available visualization options will be in the "Visualize" menu within the expanded dataset. This menu is under the small graph icon.

This is what the graph icon looks like in the Galaxy interface: http://imgur.com/a/V6PP8

Help with formatting inputs is here: https://galaxyproject.org/support/#getting-inputs-right-

Certain tools also create data visualization graphics within Galaxy as the primary or optional output. Search by the datatype name in the tool panel to locate tools that generate the desired output type. If are looking for something specific and do not find it, let us know and we can help.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
0
gravatar for mayurdoke
18 months ago by
mayurdoke10
mayurdoke10 wrote:

Hello,

Thank you for your reply. My data type is .txt and I have converted into fastaq format in Galaxy with FASTQ Groomer. After running the tool Fastqc, I could see my results about the data quality like [PASS]Basic Statistics Per base sequence quality, Per tile sequence quality, Per-sequence quality scores, Per base sequence content, Per-sequence GC content, Per base N content. But I could not see any graphs after clicking the graph icon in Galaxy interface. What is the reason behind that? Do I have to download any plugin for that? Thank you.

ADD COMMENTlink written 18 months ago by mayurdoke10

FastQC is one of those tools I mentioned that produces its own graphics. There are two outputs - one is a text report, one is a graphical report. Click on the "eye" icon for the dataset to view the graphical report in the center panel.

Guide for interpreting a FastQC report: https://galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control

Fastq data itself will not have any graphics beyond what tools generate. Other types of output (BAM, GTF, other types of different tabular data) can be graphed using the "visualize" functions. These are usually statistics (can be general stats, the same as one would graph using other methods) or data that is descriptive of where features/summary data is located, often with respect to other features, against a reference transcriptome/exome/genome.

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
0
gravatar for mayurdoke
18 months ago by
mayurdoke10
mayurdoke10 wrote:

Thanks a lot for your help.

ADD COMMENTlink written 18 months ago by mayurdoke10
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